derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

AuthorLeonardo Collado-Torres [aut, cre], Alyssa C. Frazee [ctb], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Date of publicationNone
MaintainerLeonardo Collado-Torres <lcollado@jhu.edu>
LicenseArtistic-2.0
Version1.8.0
https://github.com/lcolladotor/derfinder

View on Bioconductor

Man pages

analyzeChr: Run the derfinder analysis on a chromosome

annotateRegions: Assign genomic states to regions

calculatePvalues: Calculate p-values and identify regions

calculateStats: Calculate F-statistics at base pair resolution from a loaded...

coerceGR: Coerce the coverage to a GRanges object for a given sample

collapseFullCoverage: Collapse full coverage information for efficient quantile...

coverageToExon: Extract coverage information for exons

createBw: Export coverage to BigWig files

createBwSample: Create a BigWig file with the coverage information for a...

define_cluster: Define a cluster to use.

derfinder-deprecated: Deprecated functions in package 'derfinder'

derfinder-package: Annotation-agnostic differential expression analysis of...

extendedMapSeqlevels: Change naming style for a set of sequence names

filterData: Filter the positions of interest

findRegions: Find non-zero regions in a Rle

fullCoverage: Load the unfiltered coverage information from a group of BAM...

genomeData: Genome samples processed data

genomeDataRaw: Genome samples processed data

genomeFstats: F-statistics for the example data

genomeInfo: Genome samples information

genomeRegions: Candidate DERs for example data

genomicState: Genomic State for Hsapiens.UCSC.hg19.knownGene

getRegionCoverage: Extract coverage information for a set of regions

getTotalMapped: Calculate the total number of mapped reads

loadCoverage: Load the coverage information from a group of BAM files

makeGenomicState: Obtain the genomic state per region from annotation

makeModels: Build model matrices for differential expression

mergeResults: Merge results from different chromosomes

preprocessCoverage: Transform and split the data

railMatrix: Identify regions data by a coverage filter and get a count...

rawFiles: Construct full paths to a group of raw input files

regionMatrix: Identify regions data by a coverage filter and get a count...

sampleDepth: Calculate adjustments for library size

Files in this package

derfinder/DESCRIPTION
derfinder/NAMESPACE
derfinder/NEWS
derfinder/R
derfinder/R/Deprecated.R derfinder/R/analyzeChr.R derfinder/R/annotateRegions.R derfinder/R/calculatePvalues.R derfinder/R/calculateStats.R derfinder/R/coerceGR.R derfinder/R/collapseFullCoverage.R derfinder/R/coverageToExon.R derfinder/R/createBw.R derfinder/R/createBwSample.R derfinder/R/define_cluster.R derfinder/R/derfinder-package.R derfinder/R/extendedMapSeqlevels.R derfinder/R/filterData.R derfinder/R/findRegions.R derfinder/R/fullCoverage.R derfinder/R/genomeData-data.R derfinder/R/genomeDataRaw-data.R derfinder/R/genomeFstats-data.R derfinder/R/genomeInfo-data.R derfinder/R/genomeRegions-data.R derfinder/R/genomicState-data.R derfinder/R/getRegionCoverage.R derfinder/R/getTotalMapped.R derfinder/R/loadCoverage.R derfinder/R/makeGenomicState.R derfinder/R/makeModels.R derfinder/R/mergeResults.R derfinder/R/preprocessCoverage.R derfinder/R/railMatrix.R derfinder/R/rawFiles.R derfinder/R/regionMatrix.R derfinder/R/sampleDepth.R derfinder/R/utils.R
derfinder/README.md
derfinder/build
derfinder/build/vignette.rds
derfinder/data
derfinder/data/genomeData.RData
derfinder/data/genomeDataRaw.RData
derfinder/data/genomeFstats.RData
derfinder/data/genomeInfo.RData
derfinder/data/genomeRegions.RData
derfinder/data/genomicState.RData
derfinder/inst
derfinder/inst/CITATION
derfinder/inst/doc
derfinder/inst/doc/derfinder-quickstart.R
derfinder/inst/doc/derfinder-quickstart.Rmd
derfinder/inst/doc/derfinder-quickstart.html
derfinder/inst/doc/derfinder-users-guide.R
derfinder/inst/doc/derfinder-users-guide.Rmd
derfinder/inst/doc/derfinder-users-guide.html
derfinder/inst/extdata
derfinder/inst/extdata/chr21
derfinder/inst/extdata/chr21/annotation.Rdata
derfinder/inst/extdata/chr21/coveragePrep.Rdata
derfinder/inst/extdata/chr21/fstats.Rdata
derfinder/inst/extdata/chr21/optionsStats.Rdata
derfinder/inst/extdata/chr21/regions.Rdata
derfinder/inst/extdata/chr21/timeinfo.Rdata
derfinder/inst/extdata/genomeData
derfinder/inst/extdata/genomeData/ERR009101_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009101_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009102_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009102_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009105_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009105_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009107_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009107_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009108_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009108_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009112_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009112_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009115_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009115_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009116_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009116_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009131_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009131_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009138_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009138_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009144_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009144_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009145_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009145_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009148_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009148_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009151_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009151_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009152_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009152_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009153_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009153_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009159_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009159_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009161_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009161_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009163_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009163_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009164_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009164_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009167_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009167_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031812_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031812_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031835_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031835_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031867_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031867_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031868_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031868_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031900_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031900_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031904_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031904_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031914_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031914_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031936_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031936_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031958_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031958_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031960_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031960_accepted_hits.bam.bai
derfinder/man
derfinder/man/analyzeChr.Rd derfinder/man/annotateRegions.Rd derfinder/man/calculatePvalues.Rd derfinder/man/calculateStats.Rd derfinder/man/coerceGR.Rd derfinder/man/collapseFullCoverage.Rd derfinder/man/coverageToExon.Rd derfinder/man/createBw.Rd derfinder/man/createBwSample.Rd derfinder/man/define_cluster.Rd derfinder/man/derfinder-deprecated.Rd derfinder/man/derfinder-package.Rd derfinder/man/extendedMapSeqlevels.Rd derfinder/man/filterData.Rd derfinder/man/findRegions.Rd derfinder/man/fullCoverage.Rd derfinder/man/genomeData.Rd derfinder/man/genomeDataRaw.Rd derfinder/man/genomeFstats.Rd derfinder/man/genomeInfo.Rd derfinder/man/genomeRegions.Rd derfinder/man/genomicState.Rd derfinder/man/getRegionCoverage.Rd derfinder/man/getTotalMapped.Rd derfinder/man/loadCoverage.Rd derfinder/man/makeGenomicState.Rd derfinder/man/makeModels.Rd derfinder/man/mergeResults.Rd derfinder/man/preprocessCoverage.Rd derfinder/man/railMatrix.Rd derfinder/man/rawFiles.Rd derfinder/man/regionMatrix.Rd derfinder/man/sampleDepth.Rd
derfinder/tests
derfinder/tests/test-all.R
derfinder/tests/testthat
derfinder/tests/testthat/test_ER_level.R
derfinder/tests/testthat/test_Fstats.R
derfinder/tests/testthat/test_annotation.R
derfinder/tests/testthat/test_data.R
derfinder/tests/testthat/test_findRegions.R
derfinder/tests/testthat/test_misc.R
derfinder/vignettes
derfinder/vignettes/derfinder-quickstart.Rmd
derfinder/vignettes/derfinder-users-guide.Rmd

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